* [gentoo-commits] proj/sci:master commit in: sci-biology/amos-short/files/, sci-biology/amos-short/
@ 2011-03-06 21:16 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2011-03-06 21:16 UTC (permalink / raw
To: gentoo-commits
commit: baea040e8119bc768ba9f83cd7b82fdaab992c62
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 6 12:33:52 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 6 12:33:52 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=baea040e
sci-biology/amos-short: new package
(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)
---
sci-biology/amos-short/amos-short-0.9.3.ebuild | 34 ++++++
.../amos-short/files/amos-2.0.8-gcc44.patch | 117 ++++++++++++++++++++
sci-biology/amos-short/metadata.xml | 9 ++
3 files changed, 160 insertions(+), 0 deletions(-)
diff --git a/sci-biology/amos-short/amos-short-0.9.3.ebuild b/sci-biology/amos-short/amos-short-0.9.3.ebuild
new file mode 100644
index 0000000..484a4c3
--- /dev/null
+++ b/sci-biology/amos-short/amos-short-0.9.3.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="3"
+
+inherit eutils
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler with defaults for short reads"
+HOMEPAGE="http://amos.sourceforge.net/"
+SRC_URI="http://sourceforge.net/projects/amos/files/short_read_assembly/0.9.3/AMOS-short.tgz"
+#SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/AMOS
+
+src_prepare() {
+ epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch
+}
+
+src_compile() {
+ emake -j1 || die "emake failed"
+}
+
+src_install() {
+ emake DESTDIR="${D}" install || die "emake install failed"
+}
diff --git a/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch b/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch
new file mode 100644
index 0000000..00a37be
--- /dev/null
+++ b/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch
@@ -0,0 +1,117 @@
+diff -ur amos-2.0.8.orig/src/Align/align.cc amos-2.0.8/src/Align/align.cc
+--- amos-2.0.8.orig/src/Align/align.cc 2008-03-19 16:07:24.000000000 +0200
++++ amos-2.0.8/src/Align/align.cc 2009-07-30 19:40:51.000000000 +0300
+@@ -247,7 +247,7 @@
+ // Add incr_val to the after count in this Vote_t for ch .
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (ALPHABET, tolower (ch));
+ if (p == NULL)
+@@ -285,7 +285,7 @@
+ // count for a blank.
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (ALPHABET, tolower (ch));
+ if (p == NULL)
+@@ -357,7 +357,7 @@
+
+ {
+ int i;
+- char * p;
++ const char * p;
+
+ for (i = 0; i <= ALPHABET_SIZE; i ++)
+ here [i] = after [i] = 0;
+diff -ur amos-2.0.8.orig/src/Align/align_poly.cc amos-2.0.8/src/Align/align_poly.cc
+--- amos-2.0.8.orig/src/Align/align_poly.cc 2006-03-30 05:03:12.000000000 +0300
++++ amos-2.0.8/src/Align/align_poly.cc 2009-07-30 19:43:44.000000000 +0300
+@@ -247,7 +247,7 @@
+ // Add 1 to the after count in this Vote_t for ch .
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (ALPHABET, tolower (ch));
+ if (p == NULL)
+@@ -285,7 +285,7 @@
+ // count for a blank.
+
+ {
+- char * p;
++ const char * p;
+
+ p = strchr (ALPHABET, tolower (ch));
+ if (p == NULL)
+@@ -357,7 +357,7 @@
+
+ {
+ int i;
+- char * p;
++ const char * p;
+
+ for (i = 0; i <= ALPHABET_SIZE; i ++)
+ here [i] = after [i] = 0;
+diff -ur amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc amos-2.0.8/src/AMOS/IDMap_AMOS.cc
+--- amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc 2006-11-21 17:45:46.000000000 +0200
++++ amos-2.0.8/src/AMOS/IDMap_AMOS.cc 2009-07-30 19:30:03.000000000 +0300
+@@ -10,6 +10,7 @@
+ #include "IDMap_AMOS.hh"
+ #include <string>
+ #include <sstream>
++#include <cstdio>
+ #include <cstring>
+ using namespace AMOS;
+ using namespace std;
+diff -ur amos-2.0.8.orig/src/AMOS/Message_AMOS.cc amos-2.0.8/src/AMOS/Message_AMOS.cc
+--- amos-2.0.8.orig/src/AMOS/Message_AMOS.cc 2005-01-07 23:53:05.000000000 +0200
++++ amos-2.0.8/src/AMOS/Message_AMOS.cc 2009-07-30 19:32:21.000000000 +0300
+@@ -7,6 +7,8 @@
+ //!
+ ////////////////////////////////////////////////////////////////////////////////
+
++#include <cstdio>
++
+ #include "Message_AMOS.hh"
+ using namespace AMOS;
+ using namespace std;
+diff -ur amos-2.0.8.orig/src/Common/amp.cc amos-2.0.8/src/Common/amp.cc
+--- amos-2.0.8.orig/src/Common/amp.cc 2006-10-25 16:56:41.000000000 +0300
++++ amos-2.0.8/src/Common/amp.cc 2009-07-30 19:33:59.000000000 +0300
+@@ -1,6 +1,7 @@
+ #include "amp.hh"
+ #include <new>
+ #include <iostream>
++#include <cstdio>
+ #include <cstring>
+ #include <ctime>
+ using namespace std;
+diff -ur amos-2.0.8.orig/src/Foundation/FileSystem.cc amos-2.0.8/src/Foundation/FileSystem.cc
+--- amos-2.0.8.orig/src/Foundation/FileSystem.cc 2005-07-09 00:52:03.000000000 +0300
++++ amos-2.0.8/src/Foundation/FileSystem.cc 2009-07-30 19:35:48.000000000 +0300
+@@ -55,7 +55,7 @@
+ {
+ // Check to see if path was given
+
+- char * end_of_path = strrchr(filename, PATH_DELIMINATOR);
++ const char * end_of_path = strrchr(filename, PATH_DELIMINATOR);
+
+ if (end_of_path)
+ {
+diff -ur amos-2.0.8.orig/src/Foundation/Options.cc amos-2.0.8/src/Foundation/Options.cc
+--- amos-2.0.8.orig/src/Foundation/Options.cc 2008-06-22 18:19:07.000000000 +0300
++++ amos-2.0.8/src/Foundation/Options.cc 2009-07-30 19:37:40.000000000 +0300
+@@ -26,6 +26,7 @@
+ */
+
+ #include "Options.hh"
++#include <cstdio>
+ #include <cstring>
+
+ //! Constructor takes command line options in standard argc, argv format
diff --git a/sci-biology/amos-short/metadata.xml b/sci-biology/amos-short/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/amos-short/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/amos-short/files/, sci-biology/amos-short/
@ 2015-09-21 14:04 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2015-09-21 14:04 UTC (permalink / raw
To: gentoo-commits
commit: b4583e60fe9db0b9407413d01a36c4b72d2fe6e4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 12:33:54 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 12:33:54 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4583e60
Drop obsolete package Sources unavailable
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/amos-short/ChangeLog | 12 ---
sci-biology/amos-short/amos-short-0.9.3.ebuild | 32 ------
.../amos-short/files/amos-2.0.8-gcc44.patch | 117 ---------------------
sci-biology/amos-short/metadata.xml | 9 --
4 files changed, 170 deletions(-)
diff --git a/sci-biology/amos-short/ChangeLog b/sci-biology/amos-short/ChangeLog
deleted file mode 100644
index 9d643a4..0000000
--- a/sci-biology/amos-short/ChangeLog
+++ /dev/null
@@ -1,12 +0,0 @@
-# ChangeLog for sci-biology/amos-short
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Id$
-
- 06 Sep 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- amos-short-0.9.3.ebuild:
- sci-biology/amos-short: simplify package description
-
- 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de>
- amos-short-0.9.3.ebuild:
- Bump to EAPI=5, but drop KEYWORDS as SRC is
- unavailable
diff --git a/sci-biology/amos-short/amos-short-0.9.3.ebuild b/sci-biology/amos-short/amos-short-0.9.3.ebuild
deleted file mode 100644
index 2493899..0000000
--- a/sci-biology/amos-short/amos-short-0.9.3.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Whole genome assembler with defaults for short reads"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="http://sourceforge.net/projects/amos/files/short_read_assembly/${PV}/AMOS-short.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/AMOS
-
-src_prepare() {
- epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch
-}
-
-src_compile() {
- emake -j1
-}
-
-src_install() {
- emake DESTDIR="${D}" install
-}
diff --git a/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch b/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch
deleted file mode 100644
index 00a37be..0000000
--- a/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch
+++ /dev/null
@@ -1,117 +0,0 @@
-diff -ur amos-2.0.8.orig/src/Align/align.cc amos-2.0.8/src/Align/align.cc
---- amos-2.0.8.orig/src/Align/align.cc 2008-03-19 16:07:24.000000000 +0200
-+++ amos-2.0.8/src/Align/align.cc 2009-07-30 19:40:51.000000000 +0300
-@@ -247,7 +247,7 @@
- // Add incr_val to the after count in this Vote_t for ch .
-
- {
-- char * p;
-+ const char * p;
-
- p = strchr (ALPHABET, tolower (ch));
- if (p == NULL)
-@@ -285,7 +285,7 @@
- // count for a blank.
-
- {
-- char * p;
-+ const char * p;
-
- p = strchr (ALPHABET, tolower (ch));
- if (p == NULL)
-@@ -357,7 +357,7 @@
-
- {
- int i;
-- char * p;
-+ const char * p;
-
- for (i = 0; i <= ALPHABET_SIZE; i ++)
- here [i] = after [i] = 0;
-diff -ur amos-2.0.8.orig/src/Align/align_poly.cc amos-2.0.8/src/Align/align_poly.cc
---- amos-2.0.8.orig/src/Align/align_poly.cc 2006-03-30 05:03:12.000000000 +0300
-+++ amos-2.0.8/src/Align/align_poly.cc 2009-07-30 19:43:44.000000000 +0300
-@@ -247,7 +247,7 @@
- // Add 1 to the after count in this Vote_t for ch .
-
- {
-- char * p;
-+ const char * p;
-
- p = strchr (ALPHABET, tolower (ch));
- if (p == NULL)
-@@ -285,7 +285,7 @@
- // count for a blank.
-
- {
-- char * p;
-+ const char * p;
-
- p = strchr (ALPHABET, tolower (ch));
- if (p == NULL)
-@@ -357,7 +357,7 @@
-
- {
- int i;
-- char * p;
-+ const char * p;
-
- for (i = 0; i <= ALPHABET_SIZE; i ++)
- here [i] = after [i] = 0;
-diff -ur amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc amos-2.0.8/src/AMOS/IDMap_AMOS.cc
---- amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc 2006-11-21 17:45:46.000000000 +0200
-+++ amos-2.0.8/src/AMOS/IDMap_AMOS.cc 2009-07-30 19:30:03.000000000 +0300
-@@ -10,6 +10,7 @@
- #include "IDMap_AMOS.hh"
- #include <string>
- #include <sstream>
-+#include <cstdio>
- #include <cstring>
- using namespace AMOS;
- using namespace std;
-diff -ur amos-2.0.8.orig/src/AMOS/Message_AMOS.cc amos-2.0.8/src/AMOS/Message_AMOS.cc
---- amos-2.0.8.orig/src/AMOS/Message_AMOS.cc 2005-01-07 23:53:05.000000000 +0200
-+++ amos-2.0.8/src/AMOS/Message_AMOS.cc 2009-07-30 19:32:21.000000000 +0300
-@@ -7,6 +7,8 @@
- //!
- ////////////////////////////////////////////////////////////////////////////////
-
-+#include <cstdio>
-+
- #include "Message_AMOS.hh"
- using namespace AMOS;
- using namespace std;
-diff -ur amos-2.0.8.orig/src/Common/amp.cc amos-2.0.8/src/Common/amp.cc
---- amos-2.0.8.orig/src/Common/amp.cc 2006-10-25 16:56:41.000000000 +0300
-+++ amos-2.0.8/src/Common/amp.cc 2009-07-30 19:33:59.000000000 +0300
-@@ -1,6 +1,7 @@
- #include "amp.hh"
- #include <new>
- #include <iostream>
-+#include <cstdio>
- #include <cstring>
- #include <ctime>
- using namespace std;
-diff -ur amos-2.0.8.orig/src/Foundation/FileSystem.cc amos-2.0.8/src/Foundation/FileSystem.cc
---- amos-2.0.8.orig/src/Foundation/FileSystem.cc 2005-07-09 00:52:03.000000000 +0300
-+++ amos-2.0.8/src/Foundation/FileSystem.cc 2009-07-30 19:35:48.000000000 +0300
-@@ -55,7 +55,7 @@
- {
- // Check to see if path was given
-
-- char * end_of_path = strrchr(filename, PATH_DELIMINATOR);
-+ const char * end_of_path = strrchr(filename, PATH_DELIMINATOR);
-
- if (end_of_path)
- {
-diff -ur amos-2.0.8.orig/src/Foundation/Options.cc amos-2.0.8/src/Foundation/Options.cc
---- amos-2.0.8.orig/src/Foundation/Options.cc 2008-06-22 18:19:07.000000000 +0300
-+++ amos-2.0.8/src/Foundation/Options.cc 2009-07-30 19:37:40.000000000 +0300
-@@ -26,6 +26,7 @@
- */
-
- #include "Options.hh"
-+#include <cstdio>
- #include <cstring>
-
- //! Constructor takes command line options in standard argc, argv format
diff --git a/sci-biology/amos-short/metadata.xml b/sci-biology/amos-short/metadata.xml
deleted file mode 100644
index 07b5255..0000000
--- a/sci-biology/amos-short/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
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2011-03-06 21:16 Martin Mokrejs
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